3 papers
q-bio.QM2026
Identifying expanding TCR clonotypes with a longitudinal Bayesian mixture model and their associations with cancer patient prognosis, metastasis-directed therapy, and VJ gene enrichment
David Swanson, Alexander Sherry, Cara Haymaker +2
Examination of T-cell receptor (TCR) clonality has become a way of understanding immunologic response to cancer and its interventions in recent years. An aspect of these analyses i…
q-bio.QM2025
From Classical Machine Learning to Emerging Foundation Models: Review on Multimodal Data Integration for Cancer Research
Amgad Muneer, Muhammad Waqas, Maliazurina B Saad +16
Cancer research is increasingly driven by the integration of diverse data modalities, spanning from genomics and proteomics to imaging and clinical factors. However, extracting act…
q-bio.QM2025
The Next Layer: Augmenting Foundation Models with Structure-Preserving and Attention-Guided Learning for Local Patches to Global Context Awareness in Computational Pathology
Muhammad Waqas, Rukhmini Bandyopadhyay, Eman Showkatian +12
Foundation models have recently emerged as powerful feature extractors in computational pathology, yet they typically omit mechanisms for leveraging the global spatial structure of…